libSBML Python API
5.10.0
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{layout}
layout Class to store SBML Level, Version, and XML namespace for the SBML Layout (“layout”) package.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
SBML Level 3 “packages” add features on top of SBML Level 3 Core. When a model definition uses an SBML package, it must declare the Level and Version of SBML Core and the Version of the package being used. The package name, the SBML Level and Version, and the package Version correspond uniquely to an XML namespace added to the XML encoding of the SBML model.
LibSBML Level 3 extensions are implementations of support for SBML Level 3 packages. Each package is implemented as a separate extension. To allow software applications to query the level and version information of an extension's package implementation, libSBML uses specialized object classes. For the extension implementing the SBML “layout” package, the object class is LayoutPkgNamespaces. (This class is a specialization of a common base class called SBMLExtensionNamespaces
that is not exposed in the libSBML programming language interfaces other than C++.)
Objects of class LayoutPkgNamespaces can be passed to constructors of SBML components defined by “layout” in order to ensure that the correct component structure is created. This is necessary because different versions of an SBML Level 3 package may introduce differences in the definition of the components defined by the package. (For example, later editions of a package may introduce new attributes on a component that are not present in earlier editions of the package specification.)
Public Member Functions | |
def | addNamespace |
def | addNamespaces |
def | addPackageNamespace |
def | addPackageNamespaces |
def | clone |
def | freeSBMLNamespaces |
def | getLevel |
def | getNamespaces |
def | getPackageName |
def | getSBMLNamespaceURI |
def | getSupportedNamespaces |
def | getURI |
def | getVersion |
def | isSBMLNamespace |
def | isValidCombination |
def | removeNamespace |
def | removePackageNamespace |
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inherited |
Python method signature(s):
addNamespace(SBMLNamespaces self, string uri, string prefix)int
Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object.
uri | the XML namespace to be added. |
prefix | the prefix of the namespace to be added. |
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inherited |
Python method signature(s):
addNamespaces(SBMLNamespaces self, XMLNamespaces xmlns)int
Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object.
The following code gives an example of how one could add the XHTML namespace to the list of namespaces recorded by the top-level <sbml>
element of a model. It gives the new namespace a prefix of html
.
sbmlDoc = None try: sbmlDoc = SBMLDocument(3, 1) except ValueError: # Do something to handle exceptional situation. Candidate # causes include invalid combinations of SBML Level and Version # (impossible if hardwired as given here), running out of memory, and # unknown system exceptions. namespaces = sbmlDoc.getNamespaces() if namespaces == None: # Do something to handle case of no namespaces. status = namespaces.add('http://www.w3.org/1999/xhtml', 'html') if status != LIBSBML_OPERATION_SUCCESS: # Do something to handle failure.
xmlns | the XML namespaces to be added. |
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inherited |
Python method signature(s):
addPackageNamespace(SBMLNamespaces self, string pkgName, long pkgVersion, string prefix="")int addPackageNamespace(SBMLNamespaces self, string pkgName, long pkgVersion)
int
Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.
The SBML Level and SBML Version of this object is used.
pkgName | the string of package name (e.g. 'layout', 'multi') |
pkgVersion | the package version |
prefix | the prefix of the package namespace to be added. The package's name will be used if the given string is empty (default). |
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inherited |
Python method signature(s):
addPackageNamespaces(SBMLNamespaces self, XMLNamespaces xmlns)int
Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function).
xmlns | the XML namespaces to be added. |
def libsbml.LayoutPkgNamespaces.clone | ( | self | ) |
{layout}
layout Class to store SBML Level, Version, and XML namespace for the SBML Layout (“layout”) package.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
SBML Level 3 “packages” add features on top of SBML Level 3 Core. When a model definition uses an SBML package, it must declare the Level and Version of SBML Core and the Version of the package being used. The package name, the SBML Level and Version, and the package Version correspond uniquely to an XML namespace added to the XML encoding of the SBML model.
LibSBML Level 3 extensions are implementations of support for SBML Level 3 packages. Each package is implemented as a separate extension. To allow software applications to query the level and version information of an extension's package implementation, libSBML uses specialized object classes. For the extension implementing the SBML “layout” package, the object class is LayoutPkgNamespaces. (This class is a specialization of a common base class called SBMLExtensionNamespaces
that is not exposed in the libSBML programming language interfaces other than C++.)
Objects of class LayoutPkgNamespaces can be passed to constructors of SBML components defined by “layout” in order to ensure that the correct component structure is created. This is necessary because different versions of an SBML Level 3 package may introduce differences in the definition of the components defined by the package. (For example, later editions of a package may introduce new attributes on a component that are not present in earlier editions of the package specification.)
clone(LayoutPkgNamespaces self)LayoutPkgNamespaces
Creates and returns a deep copy of this SBMLExtensionNamespaces.
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inherited |
Python method signature(s):
freeSBMLNamespaces(List * supportedNS)
Frees the list of supported namespaces as generated by getSupportedNamespaces().
supportedNS | the list to be freed. |
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inherited |
Python method signature(s):
getLevel(SBMLNamespaces self)long getLevel(SBMLNamespaces self)
long
Get the SBML Level of this SBMLNamespaces object.
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inherited |
Python method signature(s):
getNamespaces(SBMLNamespaces self)XMLNamespaces getNamespaces(SBMLNamespaces self)
XMLNamespaces
Get the XML namespaces list for this SBMLNamespaces object.
The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them. In SBML Levels below Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.
def libsbml.LayoutPkgNamespaces.getPackageName | ( | self | ) |
Python method signature(s):
getPackageName(LayoutPkgNamespaces self)string
Returns the name of the main package for this namespace.
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inherited |
Python method signature(s):
getSBMLNamespaceURI(long level, long version)string
Returns a string representing the SBML XML namespace for the given level
and version
of SBML.
level | the SBML level |
version | the SBML version |
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inherited |
Python method signature(s):
getSupportedNamespaces()List *
Returns a list of all supported SBMLNamespaces in this version of libsbml.
def libsbml.LayoutPkgNamespaces.getURI | ( | self | ) |
Python method signature(s):
getURI(LayoutPkgNamespaces self)string
Returns a string representing the SBML XML namespace of this object.
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inherited |
Python method signature(s):
getVersion(SBMLNamespaces self)long getVersion(SBMLNamespaces self)
long
Get the SBML Version of this SBMLNamespaces object.
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inherited |
Python method signature(s):
isSBMLNamespace(string uri)bool
Predicate returning True
if the given URL is one of SBML XML namespaces.
uri | the URI of namespace |
True
if the 'uri' is one of SBML namespaces, False
otherwise.
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inherited |
Python method signature(s):
isValidCombination(SBMLNamespaces self)bool
Predicate returning True
if the given set of namespaces represent a valid set
True
if the set of namespaces is valid, False
otherwise.
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inherited |
Python method signature(s):
removeNamespace(SBMLNamespaces self, string uri)int
Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.
uri | the XML namespace to be added. |
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inherited |
Python method signature(s):
removePackageNamespace(SBMLNamespaces self, long level, long version, string pkgName, long pkgVersion)int
Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.
level | the SBML level |
version | the SBML version |
pkgName | the string of package name (e.g. 'layout', 'multi') |
pkgVersion | the package version |